Why didn’t they simply destroy the ballets?
Very likely a mailman who tossed them so as to not need to reconcile back at the orifices why the were not delivered.
Most likely because the ballots were already received and logged into their system, then subsequently ruled invalid due to bogus "technical defects". Different people are supposed to do each action. Invalid ballots should be retained for audits.
Bogus "technical defects" would show up in an audit. Batch counts would be wrong if the ballots were shredded, also leading to further investigations.
Unopened ballots thrown in the trash before reception logging would be hard to audit, but it would be hard for the clerks to know if they were throwing away the "right" ballots.
Opened ballots could easily be discarded by the clerks if the votes are "wrong". That would be pretty obvious if there were any observers present.
It would necessarily be the clerks in the election office doing this - with the cooperation of their supervisor. That is why both parties are supposed to have poll watchers in the clerks offices.